2NEF Regulatory Factor date Feb 12, 1997
title Hiv-1 Nef (Regulatory Factor), Nmr, 40 Structures
authors S.Grzesiek, A.Bax, G.M.Clore, A.M.Gronenborn, J.S.Hu, J.Kaufman, I S.J.Stahl, N.Tjandra, P.T.Wingfield
compound source
Molecule: Negative Factor (F-Protein)
Chain: A
Synonym: Hiv-1 Nef
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1
Organism_taxid: 11678
Strain: Bh10
Gene: Hiv-1 Nef
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: De3
Expression_system_plasmid: Pet11a
Expression_system_gene: Hiv-1 Nef
methodSolution NMR
note 2NEF supersedes 1NEF
related structures by homologous chain: 1AVV
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side

Primary referenceRefined solution structure and backbone dynamics of HIV-1 Nef., Grzesiek S, Bax A, Hu JS, Kaufman J, Palmer I, Stahl SJ, Tjandra N, Wingfield PT, Protein Sci 1997 Jun;6(6):1248-63. PMID:9194185
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1684 Kb) [Save to disk]
  • Biological Unit Coordinates (2nef.pdb1.gz) 43 Kb
  • CSU: Contacts of Structural Units for 2NEF
  • Retrieve 2NEF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NEF from S2C, [Save to disk]
  • View 2NEF in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2NEF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2NEF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2nef__, region [Jmol] [rasmolscript] [script source]
  • Fold representative 2nef from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nef_A] [2nef]
  • SWISS-PROT database: [Q70627]
  • Domain organization of [NEF_HV1LW] by SWISSPFAM
  • Other resources with information on 2NEF
  • Community annotation for 2NEF at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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